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Gameplay of Disruptor is similar to many first-person shooters, but the player has access to special powers called "Psionics", similar to psychokinesis. Different powers include drain, healing, shock, and a shield.

The game opens with President Krieger of Earth's United Nations talking about how he came up through the ranks of the LightStormer Corps. This turns out to be a recruiting commercial airing at the LightStormer Corps Headquarters. There, Jack Curtis, a new recruit, is talking to his elder brother and commanding officer Blake Curtis. Jack is sent on a training mission, after which he and his fellow LightStormer Troy Alexander receive psionic implants. Troy and Jack are sent on another training mission, through an "abandoned" chemical factory.

Upon returning, they are given another psionic implant, drain. Jack's third and final training mission is across several rooftops. He completes this with flying colors, then reports to Blake, who congratulates him. In fact, Jack has placed himself right up there with Blake himself... and their late father, a revered LightStormer who was a personal friend of U.N. President Krieger. Then Blake gets an emergency call, a crew of Cryo-Pirates have commandeered a space station in Jupiter's orbit. Blake sends Jack to activate the station's self-destruct sequence, which Jack does. Unbeknownst to both him and Blake, however, a mysterious girl named Eve is monitoring Jack in action and says: "This Jack Curtis might be the one we've been looking for." Back at LightStormer HQ, Blake promotes Jack to corporal for proving his value in the field; Jack has accomplished, in one mission, what took their dad three missions.

Moreover, President Krieger has taken notice of Jack and ordered an endorphine boost for him. In Blake's words, "They don't hand these out like candy." They talk briefly with Troy, who has already been promoted to sergeant and is being sent on a "special assignment" by President Krieger. Then another emergency call comes in, this time from Triton: one of Neptune's moons, where a colony of scientists was established ten years ago to terraform the moon. The colony has been overrun by hostile aliens, so Jack is dispatched to eradicate them, which he does. Returning from Triton, Jack learns that Troy has been KIA on Mars while attempting to locate a mysterious psionic orb. Blake hopes Jack will succeed where Troy failed; Jack comes through, despite having little more than his psionics to fight with, and is promoted to sergeant. Then he's sent to Antarctica to wipe out another batch of surly extraterrestrials.

This time, the results of a scientific experiment have gone haywire. For this mission, Jack receives a new psionic: shield. After this, Jack is sent to Jupiter's moon Io; retaking the colony from interplanetary gangsters who've commandeered a mine/antimatter production plant. President Krieger personally congratulates Jack upon his triumphant return, and promotes the young LightStormer to lieutenant. He then dispatches Jack to New Atlantis, to join Blake for some R&R. Just then, Blake calls in from New Atlantis. The colony has been overrun with hostiles and a reactor coolant leak is about to destroy the whole place.

Jack rushes over, outfights the enemy and kicks in the backup coolant all to no avail. New Atlantis explodes, killing Blake and thousands of innocents. Jack alone survives because Eve beamed him out of there just in time. She explains that President Krieger used Jack to locate and bring back the psionic orb, because this will give him all but unlimited power. Krieger then set up both Curtis Brothers—just as he set up their father years ago—to "tie up the loose ends." Eve is the head of a rebel faction attempting to overthrow Krieger's tyrannical Presidency and replace it with their own benevolent regime. She convinces Jack of their cause, then gives him a new psionic implant: Terrablast. Jack takes on Krieger's private army as he infiltrates the evil president's headquarters, but he gets captured by a boobytrap. Krieger uses a machine to try to retrieve the Terrablast implant from Jack's skull, but Jack resists and battles his way free of the machine. He then storms through Krieger's secret base and the rest of the evil president's forces, at last taking out Krieger. At this point, two different endings await depending on the difficulty level. In easy mode, Eve becomes President of the U.N., and Jack head of the LightStormer Corps. In hard mode, Jack himself becomes the U.N.'s new president. Either way, he gets the girl and the orb.